-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_52

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GlimmerHMM_glimmerT_59587-T1
Valid prediction for snap_scaffold_52-snap.3-T1
Couldn't classify 6242, 6285
Couldn't classify 6561, 6625
Sorry, prediction pasa_asmbl_46529.p1 fails validation.
(ATG)	 CA	5975-6083	GT	AGG
(ACT)	 AG	6242-6285	AT	GAA
(ATA)	 AC	6561-6625	GT	GTG
(TCA)	 AG	6930-7104	GG	AGG
-recovered pasa_asmbl_46529.p1, initial, 5975, 6083
-recovered pasa_asmbl_46529.p1, terminal, 6930, 7104
Valid prediction for HiQ_model.g39473.t1
Valid prediction for snap_scaffold_52-snap.2-T1
Couldn't classify 10559, 10702
Sorry, prediction pasa_asmbl_46533.p1 fails validation.
(AGG)	 CC	10559-10702	GT	TGG
(GAC)	 AG	11181-11929	GT	AGG
(GTC)	 AG	12164-12317	GT	CGG
(GTG)	 AG	12655-12834	GT	TGG
(TGG)	 AG	13235-13480	GT	CTG
(CCT)	 AG	13863-14098	GT	AGG
(CAT)	 AG	14425-14518	GT	AGG
(GTC)	 AG	14641-14725	GT	TGG
(GTA)	 AG	14881-15017	AG	AGA
-recovered pasa_asmbl_46533.p1, terminal, 14881, 15017
-recovered pasa_asmbl_46533.p1, internal, 11181, 11929
-recovered pasa_asmbl_46533.p1, internal, 12164, 12317
-recovered pasa_asmbl_46533.p1, internal, 12655, 12834
-recovered pasa_asmbl_46533.p1, internal, 13235, 13480
-recovered pasa_asmbl_46533.p1, internal, 13863, 14098
-recovered pasa_asmbl_46533.p1, internal, 14425, 14518
-recovered pasa_asmbl_46533.p1, internal, 14641, 14725
Valid prediction for snap_scaffold_52-snap.5-T1
Couldn't classify 6242, 6285
Couldn't classify 6561, 6625
Sorry, prediction CodingQuarry_transcript_52502-T1 fails validation.
(ATG)	 CA	5975-6083	GT	AGG
(ACT)	 AG	6242-6285	AT	GAA
(ATA)	 AC	6561-6625	GT	GTG
(TCA)	 AG	6930-7104	GG	AGG
-recovered CodingQuarry_transcript_52502-T1, initial, 5975, 6083
-recovered CodingQuarry_transcript_52502-T1, terminal, 6930, 7104
Valid prediction for snap_scaffold_52-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_59588-T1
Valid prediction for snap_scaffold_52-snap.6-T1
Valid prediction for HiQ_model.g39472.t1
Valid prediction for Augustus_model.g39475.t1
Valid prediction for snap_scaffold_52-snap.4-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GlimmerHMM_glimmerT_59586-T1
Valid prediction for GlimmerHMM_glimmerT_59589-T1
Couldn't classify 27479, 27644
Sorry, prediction HiQ_model.g39471.t1 fails validation.
(ATG)	 AC	23919-23996	GT	AGG
(GGT)	 AG	24078-24172	GT	AGG
(GCA)	 AG	25056-25161	GT	AGG
(GGC)	 AG	25239-25400	GT	AGG
(CTG)	 AG	25517-25602	GT	AAG
(GCT)	 AG	25685-25782	GT	CTG
(GTA)	 AG	25880-25985	GT	AGG
(GTC)	 AG	26072-26105	GT	AAG
(ATG)	 AG	26254-26390	GC	AGG
(TTA)	 AG	26497-26591	GT	AGG
(GAA)	 AG	27479-27644	GT	ATG
-recovered HiQ_model.g39471.t1, initial, 23919, 23996
-recovered HiQ_model.g39471.t1, initial, 26254, 26390
add_exon() Sorry, HiQ_model.g39471.t1 25517-25602-terminal-2 is invalid.
-recovered HiQ_model.g39471.t1, terminal, 25517, 25602
-recovered HiQ_model.g39471.t1, internal, 24078, 24172
-recovered HiQ_model.g39471.t1, internal, 25056, 25161
-recovered HiQ_model.g39471.t1, internal, 25239, 25400
-recovered HiQ_model.g39471.t1, internal, 25517, 25602
-recovered HiQ_model.g39471.t1, internal, 25685, 25782
-recovered HiQ_model.g39471.t1, internal, 25880, 25985
-recovered HiQ_model.g39471.t1, internal, 26072, 26105
-recovered HiQ_model.g39471.t1, internal, 26254, 26390
-recovered HiQ_model.g39471.t1, internal, 26497, 26591
-recovered HiQ_model.g39471.t1, internal, 27479, 27644
Couldn't classify 27479, 27612
Sorry, prediction pasa_asmbl_46521.p1 fails validation.
(ATG)	 AC	22932-23029	GT	AGG
(GAG)	 AG	23353-23686	GT	TGG
(CTG)	 AG	23841-23996	GT	AGG
(GGT)	 AG	24078-24172	GT	AGG
(GCA)	 AG	25056-25161	GT	AGG
(GGC)	 AG	25239-25400	GT	AGG
(CTG)	 AG	25517-25602	GT	AAG
(GCT)	 AG	25685-25782	GT	CTG
(GTA)	 AG	25880-25985	GT	AGG
(GTC)	 AG	26072-26105	GT	AAG
(ATG)	 AG	26254-26390	GC	AGG
(TTA)	 AG	26497-26591	GT	AGG
(GAA)	 AG	27479-27612	GT	AGG
-recovered pasa_asmbl_46521.p1, initial, 22932, 23029
-recovered pasa_asmbl_46521.p1, initial, 26254, 26390
add_exon() Sorry, pasa_asmbl_46521.p1 25517-25602-terminal-2 is invalid.
-recovered pasa_asmbl_46521.p1, terminal, 25517, 25602
-recovered pasa_asmbl_46521.p1, internal, 23353, 23686
-recovered pasa_asmbl_46521.p1, internal, 23841, 23996
-recovered pasa_asmbl_46521.p1, internal, 24078, 24172
-recovered pasa_asmbl_46521.p1, internal, 25056, 25161
-recovered pasa_asmbl_46521.p1, internal, 25239, 25400
-recovered pasa_asmbl_46521.p1, internal, 25517, 25602
-recovered pasa_asmbl_46521.p1, internal, 25685, 25782
-recovered pasa_asmbl_46521.p1, internal, 25880, 25985
-recovered pasa_asmbl_46521.p1, internal, 26072, 26105
-recovered pasa_asmbl_46521.p1, internal, 26254, 26390
-recovered pasa_asmbl_46521.p1, internal, 26497, 26591
-recovered pasa_asmbl_46521.p1, internal, 27479, 27612
Valid prediction for CodingQuarry_transcript_52501-T1
Valid prediction for snap_scaffold_52-snap.1-T1
Valid prediction for snap_scaffold_52-snap.8-T1
Valid prediction for GlimmerHMM_glimmerT_59590-T1
Valid prediction for Augustus_model.g39474.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 27771
-exon list size: 72


building trellis

1.4    
2.7    
4.1    
5.4    
6.8    
8.1    
9.5    
10.8    
12.2    
13.5    
14.9    
16.2    
17.6    
18.9    
20.3    
21.6    
23.0    
24.3    
25.7    
27.0    
28.4    
29.7    
31.1    
32.4    
33.8    
35.1    
36.5    
37.8    
39.2    
40.5    
41.9    
43.2    
44.6    
45.9    
47.3    
48.6    
50.0    
51.4    
52.7    
54.1    
55.4    
56.8    
58.1    
59.5    
60.8    
62.2    
63.5    
64.9    
66.2    
67.6    
68.9    
70.3    
71.6    
73.0    
74.3    
75.7    
77.0    
78.4    
79.7    
81.1    
82.4    
83.8    
85.1    
86.5    
87.8    
89.2    
90.5    
91.9    
93.2    
94.6    
95.9    
97.3    
98.6    
-found 6 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support